Johann Friedrich Blumenbach (1752-1840), a relatively famous eighteenth-century German anatomist and "anthropologist," published in 1786 in the second volume of his journal Medicinische Bibliothek (pp. 547-559) an essay "On the Best Methods to Collect Collectanea and Excerpts" ("Über die vorzüglichsten Methoden Collectaneen und Excerpte zu sammeln"). This essay was meant for medical practitioners, who, he felt, had a pressing need for keeping and consulting notes on medical matters in order to better treat their patients.
He finds (a priori) that a good note-taking method must have three characteristics:
1. it must allow excerpting without much loss of time
2. the excerpts must put in proper order so that one can be sure to find the excerpts or notes again
3. the excerpts or notes must be quickly retrievable when needed (548)
A posteriori, he observes that basically two methods have been followed that promise to achieve something of the sort, namely,
I. individual pieces of paper, "Zettel," or slips, and
II. indexed notebooks, or "Kollektaneenbücher" (also "Collectaneen-Bücher")
He claims that the method of making "excerpts, using scraps of paper is supported by the authority of two of the greatest scholars the world has ever seen: von Leibniz and von Haller" (549). He also claims that he has seen in the library of Hannover "perhaps a million" of such notes taken by Leibniz on scraps of paper. Both von Haller and von Leibniz carried at all times boxes of paper in order to be able to take notes.
According to Blumenbach, this method has the advantage that the slips can later be put in order at one's own leisure. It has the disadvantage, however, that the slips can easily be lost or fall into disarray. Thus he reports that a certain Stolle in Jena, who was working at his garden house on the river Saale, lost many of his notes when the wind blew the slips into the river. Therefore, a proper container is necessary. The kind of cabinet described by a certain Placcius and actually owned and used by Leibniz might be the best for such purposes. But Blumenbach finds this contraption to be fear-inspiring and "most inconvenient."
So the question arises whether one should not use a notebook instead. Again, some other famous scholars have used this method. He mentions von Boerhave and van Gorter, pointing out that the latter has described his method in a book called Methodus dirigendi studium medicum (a work I have not seen yet). According to this method, notes are taken unsystematically in the order in which one comes upon different subjects. To find things, one has therefore to create three registers: one alphabetical, one general and one special register of subject matters. Though this method secures the notes in one place, it is inconvenient as well. Blumenbach points out that the notebooks will soon become a "mess" or "Wust," and that ultimately it will be difficult to find anything in this chaos.
None of the modifications of the notebook-method solve the fundamental problems.
To record one's notes in alphabetical order is not a solution either. John Locke had described such a method in a "Lettre de Monsieur J: L. de la Societe Roiale d'Angeleterre a Monsieur N. T. contenant une methode nouvelle & facile de dresser des Recueuils, dont on peut faire un Indice exact en deux pages" in the Bibliothèque Universelle et Historique, vol. II (Amsterdam, 1686). Vincent Placcius had reported on this in his De arte excerpendi: Vom gelahrten Buchhalten liber singularis of 1689 (which also contained a description of the kind of cabinet Leibniz later used for his notes). This method is not ideal either, as things that might belong together will be separated and therefore require references to one another. Finding things thus will lead to thumbing through many pages back and forth.
Conrad Gessner's method that involves recording notes first on pieces of paper, which are then later glued into a book is also defective. Blumenbach reports that he has seen many of the numerous folio volumes with such notes in Zürich. Gluing is messy, and the resulting volumes are unshapely.
Blumenbach's alternative is not a spectacular departure from traditional methods, as he is the first to admit himself. It is rather a combination of other traditional methods. But it does meet the three a priori requirements of a good note-keeping system that formulated at the beginning of the essay, and it basically amounts to this:
1. For some of the less important subjects he recommends "durchschossene Handbücher" or textbooks with interleaved empty pages. The notes are to be placed on the pages close to the appropriate subjects of the textbook. 
2. For the main subjects Blumenbach recommends quarto pages that are folded in such a way that they form to columns. Blumenbach's advice is to write only on one side of these, and to use only one column at first. This leaves space for later additions. Every page should receive a heading that is not too general. The papers should be collected in maps or between two pages of heavy cardboard of the same format. The maps or cardboard volumes can easily be ordered and re-ordered. If a topic needs to be divided, it is easy, to separate them in one map by means of special paper, or, eventually to start a new map or cardboard folder.
The maps are placed horizontally into a small suite of pigeon holes (Fachwerk) on his writing desk. To differentiate between them, different colors for different maps or card boards should be used. (Different thickness of the maps might also do, but none of them should be thicker than a thumb.)
3. This system can be complemented with a card index and a notebook. The former can be used for preliminary notes, the latter for notes unrelated to the main subject.
In other words, Blumenbach recommends as an alternative to the slip box and the notebook, something that is the equivalent of file folders. Too bad he did not live to see the system of hanging folders, as this system may be seen as an improvement over his system of maps and files.
The article is interesting as it illustrates the different note-keeping system available to a scholar at the end of the eighteenth century.
1. It is available online here: Vorzüglichste Methode - go to page 551 of the electronic text.
2. The method of using interleaved copies of textbooks for notes and reflections was used by many scholars, including Isaac Newton and Immanuel Kant.